AMBER Archive (2008)

Subject: AMBER: Antechamber and topology file

Date: Wed Jun 11 2008 - 18:05:14 CDT

Hi there.

I am recently working on the RNA
nucleotide which has modified sugar. In order to generate force field
 , I ran the Gaussian to get the charge distribution and put Gaussian
output file into the “antechamber” to get the 'prep' and 'frcmod'
files. Based on theses information, I could get topology and initial
coordinate files for my modified nucleotide from “xleap”. During
this process, I did not get any error message nor any warning from

I placed this modified nucleotide into
larger RNA structure which has 46 residues and problem happened when
I ran the MD. The structure was getting unstable as time goes on, and
C3' endo of most residues changed to C2' endo, which is hard to
believe to happen in RNA.

In order to make sure all of procedures
so far are correct, I applied the same procedures to the normal
base-A. I put normal base-A pdb file to antechamber and get prep and
frcmod files, then ran xleap to get the topology file. I also
generated topology file directly by xleap and compared them. So, one
topology file for normal base-A was generated by antechamber
procedures and the other was pulled out from Amber data base.
Surprisingly, the information of two files are different and roughly
say, the one by antechamber has less information than the other.

Therefore, my question is how I can
generate the same topology file, for example normal base-A, by
antechamber? Are topology files for RNA (and maybe also DNA)
nucleotides specially designed in Amber, and impossible to generate
by antechamber? I tried several different ways based on the web
information, but none of these worked so far. This may be important,
because if antechamber can not generate the same (or good enough)
topology for normal base, then the topology file of modified
nucleotides may be not good enough too, and it will make the system
unstable when it substituted into larger RNA.

I attached the topology files for
normal base-A which generated by different ways.

Thank you so much.



  • application/octet-stream attachment: ra.prmtop

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